Macbook Air and "Server connections interrupted" plague.

So there is a very known issue with Airport Extremes that have hard drives connected to them and an intermitent "Server connections interrupted" popup that as far as I can tell has yet to be addressed by Apple or solved by users (there are tons of threads on the issue). The popup looks like this (not my image):

I have experienced this issue for quite a while now due to my keeping my iTunes library on the Extreme-connected hard drive and the annoyances it causes, primarily iTunes 'losing' the iTunes Media folder location in iTunes preferences and then not knowing where mp3s are and having 'broken' ⚠ song connections in iTunes, not knowing where to add new mp3s because the Media folder location is blank/empty, or most annoyingly, defaulting back to the Macbook's internal hard drive and storing new mp3s in it's iTunes Media folder, thus spreading my library across two locations/drives.

Now, for a long time I just dealt with it on my Macbook, not a big deal, but now I'm on a new MB Air and it's slim 128gb drive. I'm now moving nearly everything to the external - iTunes, iPhoto Library, Aperture library, various archive folders and reference materials, etc. and it's already beginning to really grate on my nerves. iPhoto struggles with it and losing it's library similar to how iTunes does, as do Aperture and others.

So I'm more actively looking for a solution and help. I was hoping maybe someone could think of something along the lines of Terminal, Applescript or Automator? Something that could check and maintain the connection? Or something that while those apps are open would sense when those preferences are altered due to the server interruption and restore the correct settings?

Just for the record, here is my home setup:

Airport Extreme <- External Hard Drive

Airport Extreme <- Airport Express (as extender)

Airport Extreme <- Macbook Air

Airport Extreme <- Macbook Pro

Airport Extreme <- AppleTV 2

Airport Extreme <- iPhone 3Gs & 4s